ABSTRACT Transcription factors in the nuclear factor B (NF-B) family are evolutionarily conserved master regulators of immune and inflammatory responses. They are activated in response to ligation of many receptors including T-cell receptors, B-cell receptors, members of the tumor necrosis factor (TNF) receptor superfamily and the Toll-like receptor/interleukin-1 receptor (TLR/IL-1R) superfamily. The IB kinase (IKK), comprising IKK and IKK, is at the heart of NF-B activation and mediates two NF-B activation pathways. The canonical NF-B pathway is triggered by microbial and viral infections and pro-inflammatory cytokines and is dependent on IKK phosphorylation and activation. The alternative pathway is triggered by certain members of the TNF cytokine family and selectively activates IKK. Activated IKK phosphorylates IBs, leading to their polyubiquitination and subsequent degradation by the proteasome. The freed NF-B dimers translocate to the nucleus to mediate transcription. Because of its importance in NF-B activation, IKK, especially IKK, has become a potential therapeutic target for many human diseases. The regulatory protein NEMO (also known as IKK or FIP-3) interacts with IKK and/or IKK to form the IKK, IKK or IKK/ holo-complex. The intact IKK holo-complex is approximately 700-900kD in molecular mass containing multiple copies of IKK and NEMO. IKK and IKK both contain the following conserved recognizable domains: a kinase domain (KD), a leucine zipper domain (LZ), a helix loop helix domain (HLH) and a C-terminal NEMO-binding domain (NBD). NEMO contains an N-terminal kinase-binding domain (KBD), a minimal oligomerization domain (MOD) that is also the ubiquitin binding domain (UBD) and a C-terminal zinc finger domain (ZF). IKK and NF-B signaling has attracted tremendous attention with more than 30,000 papers published on the subject. Despite the biological importance, not a single successful structure determination has been reported on IKK, an indication on the difficulty of the project. To elucidate the molecular basis of IKK function and to assist the discovery of IKK inhibitors, we propose a series of structural and functional studies on IKK, in particular, IKK and its regulatory protein NEMO.